# Source code for MDAnalysis.selections.jmol

    # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
    # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
    #
    # MDAnalysis --- https://www.mdanalysis.org
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    # Released under the Lesser GNU Public Licence, v2.1 or any higher version
    #
    # Please cite your use of MDAnalysis in published work:
    #
    # R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
    # D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
    # MDAnalysis: A Python package for the rapid analysis of molecular dynamics
    # simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
    # Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
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    # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
    # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
    # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
    #

    """
    Jmol selections
    =================

    Write :class:`MDAnalysis.core.groups.AtomGroup` selection to a `str` file
    that defines a `Jmol selection`_. To be used in Jmol_ like this::

      script macro.spt
      select ~selection

    The selection is named *mdanalysis001*.TODO

    .. autoclass:: SelectionWriter
       :inherited-members:

    .. _Jmol: http://wiki.jmol.org/index.php/Main_Page
    .. _Jmol selection: http://chemapps.stolaf.edu/jmol/docs/#define
    """
    from . import base

    class SelectionWriter(base.SelectionWriterBase):
        format = ["Jmol", "spt"]
        ext = "spt"
        default_numterms = None
        commentfmt = "#"

        def _translate(self, atoms, **kwargs):
            # Jmol indexing is 0 based when using atom bitsets
            def _index(atom):
                return str(atom.index)

            return base.join(atoms, " ", _index)

        def _write_head(self, out, **kwargs):
            out.write("@~{name!s} ({{".format(**kwargs))

        def _write_tail(self, out, **kwargs):
            out.write("});")